Intensive　marine　aquaculture　generates　complex　pollutants,　including　nutrients　and,　threatening　marine　ecosystems.　Biological　treatments　are　effective　but　vulnerable　to　disruptions,　especially　during　typhoons,　which　alter　water　quality　and　microbial　communities.　This　study　examined　a　mariculture　tailwater　(MTW)　treatment　system　in　Hainan　over　a　year,　focusing　on　seasonal　performance　in　nutrient　and　ARGs　removal,　microbial　community　dynamics,　impacts　of　environmental　changes　on　functional　microorganisms,　and　interactions　of　hosts　of　antibiotic　resistance　genes.　The　system　effectively　removed　NH4+-N　(63.74-94.73%)　during　non-typhoon　seasons,　but　typhoons　disrupted　its　nutrient　pollutant　reduction　performance.　The　proportion　of　microorganisms　involved　in　nitrogen　and　phosphorus　removal　decreased　by　changes　of　salinity　in　typhoon　events.　Antibiotic　resistance　genes　relative　abundances　were　enriched　due　to　typhoon　disaster.　The　majority　antibiotic　resistance　genes　in　the　system　were　associated　with　beta-lactam　resistance　(4.37　x　104-8.73　x　104).　Rare　bacterial　taxa　showed　the　strongest　tolerance　in　all　taxa　to　typhoon　conditions.　Archaeal　community　compositions　were　sensitive　to　these　disturbances.　Disperal　limitation　and　heterogeneous　selection　were　key　drivers　in　bacterial　and　archaeal　community　assemblies.　Microorganisms　and　antibiotic　resistance　genes　often　co-occurred　in　non-typhoon　seasons.　Vibrio　was　identified　as　a　key　potential　host　of　antibiotic　resistance　genes　in　both　seasons.　This　study　highlights　the　disruptive　effect　of　typhoons　on　the　stability　of　MTW　treatment　systems.